You're exactly right... for the original purpose - hypertext documents - HTML and CSS work just fine. The problems arise from the fact that we've hijacked these documents to produce web applications which use the barest stub of a document to get running. And then we try to shoehorn a dynamic site into what was originally designed to be a static document. Dynamic content was originally the exception, not the norm.

Frames were actually a good effort to solve the problem of web-site "chrome" (navigation bars, headers, etc), and were somewhat useful. But they proved to not be flexible enough for designers (rightly so), and thus we have the mess that we have now.